This paper describes the implementation of a widely used, bottom-up, linear programming energy systems analysis modeling framework (MARKAL) in energy sector. The definition and overview of a standard Reference Energy System (RES) structure, that illustrates how all available energy sources, energy-transforming technologies, and energy-using technologies may be utilized and combined to meet a country's energy service demands is given. The RES built for the SYNENERGY Strategic Planning Southeast Europe and Caucuses national energy models is described in detail.